Uses PLINK clumping method, where variants in LD within a particular window will be pruned. The SNP with the lowest p-value is retained.
ld_clump( dat = NULL, clump_kb = 10000, clump_r2 = 0.001, clump_p = 0.99, pop = "EUR", access_token = NULL, bfile = NULL, plink_bin = NULL )
Dataframe. Must have a variant name column ("rsid") and pval column called "pval". If id is present then clumping will be done per unique id.
Clumping kb window. Default is very strict, 10000
Clumping r2 threshold. Default is very strict, 0.001
Clumping sig level for index variants. Default = 1 (i.e. no threshold)
Super-population to use as reference panel. Default = "EUR". Options are EUR, SAS, EAS, AFR, AMR. 'legacy' also available - which is a previously used verison of the EUR panel with a slightly different set of markers
Google OAuth2 access token. Used to authenticate level of access to data
If this is provided then will use the API. Default = NULL
If null and bfile is not null then will detect packaged plink binary for specific OS. Otherwise specify path to plink binary. Default = NULL